Atomic structure of adenosine deaminase complexed with a transition-state analog: understanding catalysis and immunodeficiency mutations.

The crystal structure of a murine adenosine deaminase complexed with 6-hydroxyl-1,6-dihydropurine ribonucleoside, a nearly ideal transition-state analog, has been determined and refined at 2.4 angstrom resolution. The structure is folded as an eight-stranded parallel alpha/beta barrel with a deep pocket at the beta-barrel COOH-terminal end wherein the inhibitor and a zinc are bound and completely sequestered. The presence of the zinc cofactor and the precise structure of the bound analog were not previously known. The 6R isomer of the analog is very tightly held in place by the coordination of the 6-hydroxyl to the zinc and the formation of nine hydrogen bonds. On the basis of the structure of the complex a stereoselective addition-elimination or SN2 mechanism of the enzyme is proposed with the zinc atom and the Glu and Asp residues playing key roles. A molecular explanation of a hereditary disease caused by several point mutations of an enzyme is also presented.

[1]  F A Quiocho,et al.  Rates of ligand binding to periplasmic proteins involved in bacterial transport and chemotaxis. , 1983, The Journal of biological chemistry.

[2]  J. Hutton,et al.  Normal and mutant human adenosine deaminase genes , 1989, Journal of cellular biochemistry.

[3]  C. Ching,et al.  Identification of functional murine adenosine deaminase cDNA clones by complementation in Escherichia coli. , 1985, The Journal of biological chemistry.

[4]  N. Mcferran,et al.  Kinetics and the mechanism of action of adenosine aminohydrolase. , 1972, Biochemistry.

[5]  J. Hutton,et al.  Mutant human adenosine deaminase alleles and their expression by transfection into fibroblasts. , 1988, The Journal of biological chemistry.

[6]  M. N. Vyas,et al.  Sugar and signal-transducer binding sites of the Escherichia coli galactose chemoreceptor protein. , 1988, Science.

[7]  V. Schramm,et al.  Spontaneous epimerization of (S)-deoxycoformycin and interaction of (R)-deoxycoformycin, (S)-deoxycoformycin, and 8-ketodeoxycoformycin with adenosine deaminase. , 1985, Biochemistry.

[8]  Gregory A. Petsko,et al.  The evolution of a/ barrel enzymes , 1990 .

[9]  I. Frazer,et al.  Depressed activities of purine enzymes in lymphocytes of patients infected with human immunodeficiency virus. , 1989, Clinical chemistry.

[10]  B. C. Wang.  Resolution of phase ambiguity in macromolecular crystallography. , 1985, Methods in enzymology.

[11]  M. Sim,et al.  Studies on Adenosine Deaminase , 1971 .

[12]  R. Brady,et al.  Elevated erythrocyte adenosine deaminase activity in patients with acquired immunodeficiency syndrome. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[13]  W. Cleland,et al.  Evidence from nitrogen-15 and solvent deuterium isotope effects on the chemical mechanism of adenosine deaminase. , 1987, Biochemistry.

[14]  S. Cha,et al.  Tight-binding inhibitors-II. Non-steady state nature of inhibition of milk xanthine oxidase by allopurinol and alloxanthine and of human erythrocytic adenosine deaminase by coformycin. , 1975, Biochemical pharmacology.

[15]  D. Bonthron,et al.  Identification of a point mutation in the adenosine deaminase gene responsible for immunodeficiency. , 1985, The Journal of clinical investigation.

[16]  R. Parks,et al.  Adenosine metabolism in human whole blood. Effects of nucleoside transport inhibitors and phosphate concentration. , 1988, Biochemical pharmacology.

[17]  B. Lee,et al.  The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.

[18]  T. Knudsen,et al.  Developmental expression of adenosine deaminase in the upper alimentary tract of mice. , 1990, Differentiation; research in biological diversity.

[19]  A. C. Chinault,et al.  Deduced amino acid sequence of Escherichia coli adenosine deaminase reveals evolutionarily conserved amino acid residues: implications for catalytic function. , 1991, Biochemistry.

[20]  R. Wolfenden,et al.  Substrate binding by adenosine deaminase. Specificity, pH dependence, and competition by mercurials. , 1967, The Journal of biological chemistry.

[21]  A. Wauquier,et al.  The nucleoside-transport inhibitor soluflazine (R 64 719) increases the effects of adenosine in the guinea-pig hippocampal slice and is antagonized by adenosine deaminase. , 1987, European journal of pharmacology.

[22]  R. Wolfenden,et al.  Ring-modified substrates of adenosine deaminases. , 1969, Biochemistry.

[23]  G. Petsko,et al.  Transition-state analogues in protein crystallography: probes of the structural source of enzyme catalysis. , 1990, Annual review of biochemistry.

[24]  E. Gelfand,et al.  Biochemistry of diseases of immunodevelopment. , 1981, Annual review of biochemistry.

[25]  J. Hutton,et al.  Mutations in the human adenosine deaminase gene that affect protein structure and RNA splicing. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[26]  P. J. Harper,et al.  Substrate properties of cycloadenosines with adenosine aminohydrolase as evidence for the conformation of enzyme-bound adenosine. , 1972, Biochemistry.

[27]  B. E. Evans,et al.  Catalysis of the covalent hydration of pteridine by adenosine aminohydrolase. , 1973, Biochemistry.

[28]  P. C. Lee.  Developmental changes of adenosine deaminase, xanthine oxidase, and uricase in mouse tissues. , 1973, Developmental biology.

[29]  R. Wolfenden,et al.  Transition state stabilization by deaminases: Rates of nonenzymatic hydrolysis of adenosine and cytidine , 1987 .

[30]  M. Karplus,et al.  Crystallographic R Factor Refinement by Molecular Dynamics , 1987, Science.

[31]  F. Quiocho,et al.  Preliminary X-ray analysis of crystals of murine adenosine deaminase. , 1988, Journal of molecular biology.

[32]  R. Agarwal.  Inhibitors of adenosine deaminase. , 1982, Pharmacology & therapeutics.

[33]  R. Hirschhorn,et al.  Identification of a point mutation resulting in a heat-labile adenosine deaminase (ADA) in two unrelated children with partial ADA deficiency. , 1989, The Journal of clinical investigation.

[34]  R. Wolfenden,et al.  Major enhancement of the affinity of an enzyme for a transition-state analog by a single hydroxyl group. , 1989, Science.

[35]  Carl Frieden,et al.  Adenosine deaminase converts purine riboside into an analogue of a reactive intermediate: a 13C NMR and kinetic study. , 1987, Biochemistry.

[36]  Brian W. Matthews,et al.  Structural basis of the action of thermolysin and related zinc peptidases , 1988 .

[37]  F. A. Quiocho,et al.  Substrate specificity and affinity of a protein modulated by bound water molecules , 1989, Nature.

[38]  Carl Frieden,et al.  Adenosine deaminase: solvent isotope and pH effects on the binding of transition-state and ground-state analogue inhibitors. , 1983, Biochemistry.

[39]  P. W. Woo,et al.  A novel adenosine and ara‐a deaminase inhibitor, (R)‐3‐(2‐deoxy‐β‐D‐erythro‐pentofuranosyl)‐3,6,7,8‐tetrahydroimidazo[4,5 ‐d] [1,3]diazepin‐8‐ol , 1974 .